Assuming Nvidia. This is how you actually add custom resolutions, the way you described your issue makes it sound like it isn't this but it's worth checking anyways
right click the desktop
http://puu.sh/bnRbx/0df468b62e.png
click nvidia control panel
click change resolution on the left bar thing here
http://puu.sh/bnRdc/6fe4a75931.png
click customize here
http://puu.sh/bnRgv/7c8222e789.png
click 'create custom resolution'
http://puu.sh/bnRh8/ff44179a94.png
make your settings whatever you want them and whatever isn't out of your monitor's display range
http://puu.sh/bnRjh/e37db182a8.png
If it's an issue beyond that as you described in your OP, I used to have this issue. My (shitty) solution was to downgrade to 182.50 nvidia drivers (the last drivers before some 3d-related stuff was added iirc, could be totally wrong though). I didn't have to do this for over a year now though, currently on 340.52
Another possibility - when I play a game in fullscreen that changes my resolution it sets my refresh rate back to 85Hz every time